Aquatic Microbiology
Most of the Earth is covered in a layer of water. These aquatic environments are often separated into oceans and
inland waters. Oceans cover nearly 70% of the Earth’s surface and comprise approximately 97% of the total amount
of water on the planet. Depths may vary from 200m at the continental shelf to 10,000m or more at the trenches.
Since 90% of the world’s oceans are deeper than 1000m, conditions of low temperatures a few degrees above
freezing, elevated hydrostatic pressure (1 atmosphere/10m depth), and near-total darkness prevails. Salinity of water
varies between 32o/oo (parts per thousand) to 38o/oo, with an average of 35o/oo. Although the surface of ocean
water is subject to evaporation and movement through the hydrologic cycle, the average residence time of water in
the ocean is thousands of years.
Inland waters are classified as subterranean (ground-) and surface waters. Groundwater accounts for 0.3 to 0.8 %
of the total water amount. Groundwater is contained in the permeable rocks below the water table and accumulates as
it (vadose water) percolates through the overlying soil. Groundwater is considered oligotrophic (low nutrient content
in proportion to water) since most of the nutrients are lost through ground filtration. Once in the ground, water has an
average residence time of 100 to 1000s of years. Overdraft of water occurs when use is greater than replenish rate.
The resulting consequences of overdraft of groundwater include sinkholes, salt water intrusion, destruction of
effluent streams and riparian vegetation, and subsidence (sinking) of land. Approximately 50% (35% municipal, 95%
rural) of the U.S. population depend on groundwater for drinking. Recently, it was estimated that 75% of known the
175,000 waste disposal sites in the U.S. have seepage into the surrounding ground and aquifer. With 90 of organics
unidentified or quantified in landfill leachates, the public health implications are unknown.
Surface waters include lotic, or running, water (springs, streams, and rivers), and standing, or lentic, waters (lakes,
ponds, swamps, bogs). Lotic and lentic waters account for 0.0001 % and 0.009 % of the total water pool,
respectively. When groundwater breaks the surface, it is called a spring. Springs are also oligotrophic except for
specialized springs including mineral springs and hot springs, which contain accumulations of dissolved minerals and
gases. Springs, groundwater seepage, and land runoff and precipitation form rivers. The mineral and organic
components of a river are often dependent on the nature of the land it runs through. Rivers eventually empty into
seawater at a basin called an estuary, or into lakes.
Lentic waters are diverse in size, depth, and other physical features. A small pond may be 10m deep compared to
1741m of depth in Lake Baikal, Siberia. The separation between lake and pond is somewhat ambiguous, but
generally, vegetation occurs throughout the bottom of a pond, whereas lakes are too deep to support the growth of
submerged plants. Lakes (and oceans) in temperate latitudes tend to become stratified during warmer months. The
upper layers, called the epilimnion, become warmer and less dense than the lower, colder layer called a
hypolimnion. The boundary between these two layers is the thermocline and vertical mixing is minimized. Water
received into a lentic system may remain there for tens of years whereas in lotic systems, residence is approximately
two weeks. The remaining 2% of water not yet discussed is maintained as polar ice and glaciers. Lakes are often
created through glacial action (or movements in the Earth’s crust) or geological events, but once formed, begin to
change through sedimentation and rim erosion until it is leveled and filled. Once water becomes frozen as glacier or
polar ice, it may remain as such for tens of thousands of years. Approximately .001% is atmospheric moisture with a
residence time of 9 days.
Despite the variety of conditions that prevail in aquatic habitats, microorganisms are found in nearly all aquatic
environments from the smallest of ponds to the largest, deepest oceans. Aquatic microbiology is the study of
microorganisms which live in the Earth’s natural bodies of water. Microorganisms, or phytoplankton, including
bacteria, algae, and fungi make up a large portion of the total biomass in all aquatic environments. The microbiota of
aquatic systems is both autochthonous (residents) and allochthonous (transported from another location), although
microbes originating from other environments quickly die-off. Microbial composition of a water system depends on
both physical, chemical, and nutritional conditions.
Planktonic microalgae, and to some lesser extent photosynthetic bacteria, are the most important primary producers
in aquatic systems. In small bodies of water, such as ponds, benthic algae and spermatophytes are the major primary
producers; however, in larger bodies of water, including lakes and oceans, the algal phytoplankton are the main
primary producer. In freshwater, the cyanobacteria, green algae (Chlorophyta), and yellow-brown algae
(Chrysophyta) including diatoms, predominate. The diatoms and other chrysophyta and dinoflagellates (Pyrrophyta)
predominate in seawater. Distribution of algae is primarily determined by environmental factors such as light,
temperature, and nutrient supply. Slow moving or stagnant waters favor growth of planktonic algae. Rapid growth
and accumulation of cells are called blooms (neuston). In lotic waters (fast-flowing), the microalgae are epilithic,
growing on stones or other submerged debris, or benthic, living in the bottom sediment.
Chemoautotrophic bacteria are widely distributed throughout aquatic systems, both in the water column, in
sediments, and as symbionts of some aquatic animals. These organisms are the sole primary producers of organic
material in aquatic habitats devoid of sunlight, and volcanic vent habitats. A number of reduced substances,
including iron, sulfur, hydrogen gas, and nitrogen, are utilized by these organisms. Many of these reduced substances
are produced under anaerobic conditions that prevail in sediment, therefore, chemoautotrophic bacteria are
commonly present at the boundary between reduced and oxygenated regions in sediment. These bacteria are a
critical component in nutrient recycling.
Heterotrophs form the greater percentage of microorganisms in aquatic systems. The species of heterotrophs and
population densities is largely dependent on nutrient availability. In nutrient poor groundwater or springs, the
number of heterotrophic bacteria are low, probably in the range of a few thousand cells/ml. Along the course of the
stream, as nutrient content increases, the populations and diversity of bacteria also increase. The bacterial
populations of streams and rivers show a close relationship with the surrounding terrestrial microorganisms, because
of the constant injection of soil, water runoff, and organic material into the water. Many of these microbes are
allochthonous. Lakes and ponds are more self-contained than lotic waters, and thus a larger percentage of microbiota
are autochthonous. Vertical distribution of bacteria varies seasonally with stratification and availability of nutrients.
A distinguishing feature between marine bacteria and those found in freshwater and terrestrial habitats is a specific
requirement for sodium, which in many cases is necessary for the transport of substances into the cell. The highest
numbers of marine heterotrophs are found in nutrient rich areas including near shore waters and in sediments.
All divisions of fungi are found in aquatic environments, either free-living or, more likely, growing on surfaces. The
subdivision Chytridiomycetes and similar fungal-like organisms called water molds (Oomycetes) are important
saprophytes found in most aquatic environments. A few species are parasites of plants and animals. The distribution
and numbers of fungi are dependent upon the presence of the plants and animals they parasitize or consume when
dead. Therefore, oligotrophic water such as groundwater and springs are not suitable for fungal growth, whereas in
the more eutrophic waters such as rivers, ponds, lakes, and near shore oceans, they are usually abundant and critical
as decomposers.
Pollution greatly affects microbial populations and water quality. A pollutant is generally defined as any chemical,
physical or biological factor that when present in excess causes harm to other living organisms. Nine broad
categories of pollutants are recognized. The effects on aquatic life and the organisms that use the water resources
vary due to differences in tolerance ranges and physiology of each organism. The catgories are:
1. Dead organic matter: sewage, agricultural waste and garbage
2. Pathogens: water borne bacteria, viruses and protozoa that cause disease
3. Organic chemicals: pesticides, herbicides, dioxin, polyaromatic hydrocarbons
4. Nutrients: nitrogen, phosphorous
5. Heavy metals: arsenic, lead, cadmium, mercury, copper, selenium
6. Acids: sulfuric and nitric
7. Sediment: top soil and stream bank erosion
8. Thermal pollution: heated water discharge
9. Radioactivity: radioisotopes from mining, military and accidents
Of these categories, sedimentation is the leading pollution problem in the U.S. Bodies of water surrounding agricultural
lands are subject to several categories of pollutants including organic matter, organic chemicals, nutrients and sediments.
Acidification due to acid precipitation primarily occurs in areas with coal burning power plants and steel mills.